QC Report

	general
Report generated at	2019-12-05 12:55:15
Title	BY4742--MSS11
Description	chipseq of yeast BY4742 for tf MSS11
Pipeline version	v1.3.3
Pipeline type	tf
Genome	BY4742
Paired-end per replicate	[True, True]
Aligner	bowtie2
Peak caller	spp
Control paired-end per replicate	[True, True, True, True]

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Total Reads	7061572	6399676	4555882	6930446	9302162	7321170
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	5186762	4870594	4209856	6142696	8516629	6004918
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	73.5	76.1	92.4	88.6	91.60000000000001	82.0
Paired Reads	7061572	6399676	4555882	6930446	9302162	7321170
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	3530786	3199838	2277941	3465223	4651081	3660585
Read1 (QC-failed)	0	0	0	0	0	0
Read2	3530786	3199838	2277941	3465223	4651081	3660585
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	4136992	4041666	3408530	4817860	6865532	4002636
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	58.599999999999994	63.2	74.8	69.5	73.8	54.7
With itself	5077146	4731340	4169336	6059104	8426516	5323690
With itself (QC-failed)	0	0	0	0	0	0
Singletons	109616	139254	40520	83592	90113	681228
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	1.6	2.1999999999999997	0.8999999999999999	1.2	1.0	9.3
Diff. Chroms	4136	4690	1815	2127	4171	2235
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Unpaired Reads	0	0	0	0	0	0
Paired Reads	1477295	1375891	1476158	2070343	2961014	1730516
Unmapped Reads	0	0	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0	0	0
Paired Duplicate Reads	28091	26326	3321	7880	13554	5282
Paired Optical Duplicate Reads	426	367	552	549	1092	1711
% Duplicate Reads	1.9015	1.9134000000000002	0.22499999999999998	0.3806	0.45770000000000005	0.3052

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Total Reads	2898408	2699130	2945674	4124926	5894920	3450468
Total Reads (QC-failed)	0	0	0	0	0	0
Duplicate Reads	0	0	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0	0	0
Mapped Reads	2898408	2699130	2945674	4124926	5894920	3450468
Mapped Reads (QC-failed)	0	0	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0	100.0	100.0
Paired Reads	2898408	2699130	2945674	4124926	5894920	3450468
Paired Reads (QC-failed)	0	0	0	0	0	0
Read1	1449204	1349565	1472837	2062463	2947460	1725234
Read1 (QC-failed)	0	0	0	0	0	0
Read2	1449204	1349565	1472837	2062463	2947460	1725234
Read2 (QC-failed)	0	0	0	0	0	0
Properly Paired Reads	2898408	2699130	2945674	4124926	5894920	3450468
Properly Paired Reads (QC-failed)	0	0	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0	100.0	100.0
With itself	2898408	2699130	2945674	4124926	5894920	3450468
With itself (QC-failed)	0	0	0	0	0	0
Singletons	0	0	0	0	0	0
Singletons (QC-failed)	0	0	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0	0	0
Diff. Chroms (QC-failed)	0	0	0	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1	ctl2	ctl3	ctl4
Total Fragments	1461746	1366689	1449951	2021943	2908895	1705713
Distinct Fragments	1434025	1340581	1446811	2014504	2895991	1700692
Positions with Two Read	25562	24168	3114	7276	12643	4962
NRF = Distinct/Total	0.981036	0.980897	0.997834	0.996321	0.995564	0.997056
PBC1 = OneRead/Distinct	0.981476	0.981295	0.997839	0.996349	0.99559	0.997065
PBC2 = OneRead/TwoRead	55.060676	54.431687	463.61079	275.858988	228.048723	341.737404

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	2019	854
N1	1723	569
N2	1737	606
Np	2082	660
N optimal	2082	854
N conservative	2019	854
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0312035661218424	1.293939393939394
Self Consistency Ratio	1.008125362739408	1.0650263620386644
Reproducibility Test	pass	pass

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Number of raw peaks

	rep1	rep2
Number of peaks	3644	3666

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	90.0	91.0	109.0	109.0
25 percentile	360.0	364.0	363.0	436.0
50 percentile (median)	360.0	364.0	433.0	436.0
75 percentile	360.0	364.0	459.0	436.0
Max size	758.0	733.0	2122.0	2122.0
Mean	352.49560922063665	355.8829787234043	443.0128805620609	431.26464937560036

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	1979130	1661752
Estimated Fragment Length	135	155
Cross-correlation at Estimated Fragment Length	0.832021625714446	0.807335719470109
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.8204745	0.783757
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7697646	0.7265481
NSC (Normalized Strand Cross-correlation coeff.)	1.080878	1.111194
RSC (Relative Strand Cross-correlation coeff.)	1.22771	1.412152

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.34270433976168985	0.3770377862496434	0.35181727348254627	0.38669913142447276	0.3447244142301567	0.3857208698513001	0.35315651273827886	0.3544482040324857	0.36343383946079133

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.3056758167608688	0.27112573523120276	0.3059682193892106	0.30858531018458474

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.24696536227177018	0.20064255963963665	0.23720013485826916	0.23123594694667549

For spp raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates